diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix
index 288ffd6e0e1..098ce3925cf 100644
--- a/pkgs/applications/science/math/sage/env-locations.nix
+++ b/pkgs/applications/science/math/sage/env-locations.nix
@@ -38,6 +38,7 @@ writeTextFile rec {
export COMBINATORIAL_DESIGN_DATA_DIR="${combinatorial_designs}/share/combinatorial_designs"
export CREMONA_MINI_DATA_DIR="${elliptic_curves}/share/cremona"
export JMOL_DIR="${jmol}"
+ export JSMOL_DIR="${jmol}/share/jsmol"
export MATHJAX_DIR="${mathjax}/lib/node_modules/mathjax"
export THREEJS_DIR="${three}/lib/node_modules/three"
export SAGE_INCLUDE_DIRECTORIES="${cysignals}/lib/python2.7/site-packages"
diff --git a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch b/pkgs/applications/science/math/sage/patches/dochtml-optional.patch
deleted file mode 100644
index a51e30312ed..00000000000
--- a/pkgs/applications/science/math/sage/patches/dochtml-optional.patch
+++ /dev/null
@@ -1,127 +0,0 @@
-diff --git a/src/doc/common/conf.py b/src/doc/common/conf.py
-index 25f94f7b7d..9f6139ea4a 100644
---- a/src/doc/common/conf.py
-+++ b/src/doc/common/conf.py
-@@ -622,9 +622,9 @@ def call_intersphinx(app, env, node, contnode):
- Check that the link from the thematic tutorials to the reference
- manual is relative, see :trac:`20118`::
-
-- sage: from sage.env import SAGE_DOC
-- sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html")
-- sage: for line in open(thematic_index).readlines():
-+ sage: from sage.env import SAGE_DOC # optional - dochtml
-+ sage: thematic_index = os.path.join(SAGE_DOC, "html", "en", "thematic_tutorials", "index.html") # optional - dochtml
-+ sage: for line in open(thematic_index).readlines(): # optional - dochtml
- ....: if "padics" in line:
- ....: sys.stdout.write(line)
- Introduction to the -adics
-diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py
-index 4236fd05e0..8e499cbaf7 100644
---- a/src/sage/doctest/control.py
-+++ b/src/sage/doctest/control.py
-@@ -87,7 +87,7 @@ class DocTestDefaults(SageObject):
- self.sagenb = False
- self.long = False
- self.warn_long = None
-- self.optional = set(['sage']) | auto_optional_tags
-+ self.optional = set(['sage', 'dochtml']) | auto_optional_tags
- self.randorder = None
- self.global_iterations = 1 # sage-runtests default is 0
- self.file_iterations = 1 # sage-runtests default is 0
-@@ -343,7 +343,8 @@ class DocTestController(SageObject):
- if not optionaltag_regex.search(o):
- raise ValueError('invalid optional tag {!r}'.format(o))
-
-- options.optional |= auto_optional_tags
-+ if "sage" in options.optional:
-+ options.optional |= auto_optional_tags
-
- self.options = options
- self.files = args
-@@ -741,7 +742,7 @@ class DocTestController(SageObject):
- sage: DC = DocTestController(DD, [dirname])
- sage: DC.expand_files_into_sources()
- sage: sorted(DC.sources[0].options.optional) # abs tol 1
-- ['guava', 'magma', 'py3']
-+ ['guava', 'magma']
-
- We check that files are skipped appropriately::
-
-@@ -968,7 +969,7 @@ class DocTestController(SageObject):
- sage: from sage.doctest.control import DocTestDefaults, DocTestController
- sage: DC = DocTestController(DocTestDefaults(), [])
- sage: DC._optional_tags_string()
-- 'sage'
-+ 'dochtml,sage'
- sage: DC = DocTestController(DocTestDefaults(optional="all,and,some,more"), [])
- sage: DC._optional_tags_string()
- 'all'
-diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
-index 9255aa848f..cc4712d3ec 100644
---- a/src/sage/misc/sagedoc.py
-+++ b/src/sage/misc/sagedoc.py
-@@ -18,9 +18,9 @@ TESTS:
- Check that argspecs of extension function/methods appear correctly,
- see :trac:`12849`::
-
-- sage: from sage.env import SAGE_DOC
-- sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html')
-- sage: with open(docfilename) as fobj:
-+ sage: from sage.env import SAGE_DOC # optional - dochtml
-+ sage: docfilename = os.path.join(SAGE_DOC, 'html', 'en', 'reference', 'calculus', 'sage', 'symbolic', 'expression.html') # optional - dochtml
-+ sage: with open(docfilename) as fobj: # optional - dochtml
- ....: for line in fobj:
- ....: if "#sage.symbolic.expression.Expression.numerical_approx" in line:
- ....: print(line)
-@@ -790,11 +790,12 @@ def _search_src_or_doc(what, string, extra1='', extra2='', extra3='',
-
- ::
-
-- sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1
-+ sage: from sage.misc.sagedoc import _search_src_or_doc # optional - dochtml
-+ sage: len(_search_src_or_doc('src', r'matrix\(', 'incidence_structures', 'self', 'combinat', interact=False).splitlines()) > 1 # optional - dochtml
- True
-- sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False) # long time (4s on sage.math, 2012)
-+ sage: 'abvar/homology' in _search_src_or_doc('doc', 'homology', 'variety', interact=False) # optional - dochtml, long time (4s on sage.math, 2012)
- True
-- sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False)
-+ sage: 'divisors' in _search_src_or_doc('src', '^ *def prime', interact=False) # optional - dochtml
- True
- """
- # process keywords
-@@ -1160,9 +1161,9 @@ def search_doc(string, extra1='', extra2='', extra3='', extra4='',
- counting the length of ``search_doc('tree',
- interact=False).splitlines()`` gives the number of matches. ::
-
-- sage: len(search_doc('tree', interact=False).splitlines()) > 4000 # long time
-+ sage: len(search_doc('tree', interact=False).splitlines()) > 4000 # optional - dochtml, long time
- True
-- sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000 # long time
-+ sage: len(search_doc('tree', whole_word=True, interact=False).splitlines()) < 2000 # optional - dochtml, long time
- True
- """
- return _search_src_or_doc('doc', string, extra1=extra1, extra2=extra2,
-@@ -1332,9 +1333,9 @@ class _sage_doc:
-
- EXAMPLES::
-
-- sage: browse_sage_doc._open("reference", testing=True)[0] # indirect doctest
-+ sage: browse_sage_doc._open("reference", testing=True)[0] # optional - dochtml, indirect doctest
- 'http://localhost:8000/doc/live/reference/index.html'
-- sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47]
-+ sage: browse_sage_doc(identity_matrix, 'rst')[-107:-47] # optional - dochtml
- 'Full MatrixSpace of 3 by 3 sparse matrices over Integer Ring'
- """
- def __init__(self):
-@@ -1494,9 +1495,9 @@ class _sage_doc:
-
- EXAMPLES::
-
-- sage: browse_sage_doc._open("reference", testing=True)[0]
-+ sage: browse_sage_doc._open("reference", testing=True)[0] # optional - dochtml
- 'http://localhost:8000/doc/live/reference/index.html'
-- sage: browse_sage_doc._open("tutorial", testing=True)[1]
-+ sage: browse_sage_doc._open("tutorial", testing=True)[1] # optional - dochtml
- '.../html/en/tutorial/index.html'
- """
- url = self._base_url + os.path.join(name, "index.html")
diff --git a/pkgs/applications/science/math/sage/patches/eclib-20180710.patch b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
index d06e1e6cedf..986ae42aeb6 100644
--- a/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
+++ b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch
@@ -14,27 +14,3 @@ index 4417b59276..ae57ca2991 100644
"""
global instances
try:
-diff --git a/src/sage/libs/eclib/wrap.cpp b/src/sage/libs/eclib/wrap.cpp
-index 5fd5693b53..d12468faa8 100644
---- a/src/sage/libs/eclib/wrap.cpp
-+++ b/src/sage/libs/eclib/wrap.cpp
-@@ -133,8 +133,8 @@ char* Curvedata_isogeny_class(struct Curvedata* E, int verbose)
-
-
- int mw_process(struct Curvedata* curve, struct mw* m,
-- const struct bigint* x, const struct bigint* y,
-- const struct bigint* z, int sat)
-+ const bigint* x, const bigint* y,
-+ const bigint* z, int sat)
- {
- Point P(*curve, *x, *y, *z);
- if (!P.isvalid())
-@@ -188,7 +188,7 @@ int mw_rank(struct mw* m)
- }
-
- /* Returns index and unsat long array, which user must deallocate */
--int mw_saturate(struct mw* m, struct bigint* index, char** unsat,
-+int mw_saturate(struct mw* m, bigint* index, char** unsat,
- long sat_bd, int odd_primes_only)
- {
- vector v;
diff --git a/pkgs/applications/science/math/sage/patches/pari-no-threads.patch b/pkgs/applications/science/math/sage/patches/pari-no-threads.patch
deleted file mode 100644
index 13b47dbdd31..00000000000
--- a/pkgs/applications/science/math/sage/patches/pari-no-threads.patch
+++ /dev/null
@@ -1,18 +0,0 @@
-diff --git a/src/sage/libs/pari/__init__.py b/src/sage/libs/pari/__init__.py
-index e451766474..77eda66097 100644
---- a/src/sage/libs/pari/__init__.py
-+++ b/src/sage/libs/pari/__init__.py
-@@ -205,6 +205,13 @@ def _get_pari_instance():
- # messages in Sage.
- P.default("debugmem", 0)
-
-+ # Make sure pari doesn't use threads, regardless of how it was compiled.
-+ # Threads cause some doctest failures (memory issues). Those could probably
-+ # be solved without disabling threads. But that would require figuring out
-+ # some sensible values for `threadsizemax`. See
-+ # https://pari.math.u-bordeaux.fr/dochtml/html/GP_defaults.html
-+ P.default("nbthreads", 1)
-+
- return P
-
- pari = _get_pari_instance()
diff --git a/pkgs/applications/science/math/sage/patches/singular-4.1.1p2.patch b/pkgs/applications/science/math/sage/patches/singular-4.1.1p2.patch
deleted file mode 100644
index 4c8df92904e..00000000000
--- a/pkgs/applications/science/math/sage/patches/singular-4.1.1p2.patch
+++ /dev/null
@@ -1,274 +0,0 @@
-diff --git a/src/sage/interfaces/singular.py b/src/sage/interfaces/singular.py
-index 9d65c9fa6c..a028bbe719 100644
---- a/src/sage/interfaces/singular.py
-+++ b/src/sage/interfaces/singular.py
-@@ -654,7 +654,7 @@ class Singular(ExtraTabCompletion, Expect):
-
- s = Expect.eval(self, x, **kwds)
-
-- if s.find("error") != -1 or s.find("Segment fault") != -1:
-+ if s.find("error occurred") != -1 or s.find("Segment fault") != -1:
- raise SingularError('Singular error:\n%s'%s)
-
- if get_verbose() > 0:
-@@ -1079,7 +1079,7 @@ class Singular(ExtraTabCompletion, Expect):
- sage: S = singular.ring('real', '(a,b)', 'lp')
- sage: singular.current_ring()
- polynomial ring, over a field, global ordering
-- // coefficients: float
-+ // coefficients: Float()
- // number of vars : 2
- // block 1 : ordering lp
- // : names a b
-@@ -1157,7 +1157,7 @@ class Singular(ExtraTabCompletion, Expect):
- sage: singular._tab_completion()
- ['exteriorPower',
- ...
-- 'flintZ']
-+ 'crossprod']
- """
- p = re.compile("// *([a-z0-9A-Z_]*).*") #compiles regular expression
- proclist = self.eval("listvar(proc)").splitlines()
-@@ -1183,7 +1183,7 @@ class Singular(ExtraTabCompletion, Expect):
- EXAMPLES::
-
- sage: singular.version()
-- "Singular ... version 4.1.0 ...
-+ "Singular ... version 4...
- """
- return singular_version()
-
-@@ -1562,7 +1562,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement):
- elif charstr[0] in ['0', 'QQ']:
- from sage.all import QQ
- br = QQ
-- elif charstr[0]=='real':
-+ elif charstr[0].startswith('Float'):
- from sage.all import RealField, ceil, log
- prec = singular.eval('ringlist(basering)[1][2][1]')
- br = RealField(ceil((ZZ(prec)+1)/log(2,10)))
-@@ -1750,7 +1750,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement):
-
- # Singular 4 puts parentheses around floats and sign outside them
- charstr = self.parent().eval('charstr(basering)').split(',',1)
-- if charstr[0] in ['real', 'complex']:
-+ if charstr[0]=='complex' or charstr[0].startswith('Float'):
- for i in range(coeff_start, 2 * coeff_start):
- singular_poly_list[i] = singular_poly_list[i].replace('(','').replace(')','')
-
-@@ -1992,7 +1992,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement):
- sage: S = singular.ring('real', '(a,b)', 'lp')
- sage: singular.current_ring()
- polynomial ring, over a field, global ordering
-- // coefficients: float
-+ // coefficients: Float()
- // number of vars : 2
- // block 1 : ordering lp
- // : names a b
-@@ -2072,7 +2072,7 @@ class SingularElement(ExtraTabCompletion, ExpectElement):
- sage: R._tab_completion()
- ['exteriorPower',
- ...
-- 'flintZ']
-+ 'crossprod']
- """
- return self.parent()._tab_completion()
-
-@@ -2358,7 +2358,7 @@ def singular_version():
- EXAMPLES::
-
- sage: singular.version()
-- "Singular ... version 4.1.0 ...
-+ "Singular ... version 4...
- """
- return singular.eval('system("--version");')
-
-diff --git a/src/sage/libs/singular/decl.pxd b/src/sage/libs/singular/decl.pxd
-index 4b658c4807..d863740419 100644
---- a/src/sage/libs/singular/decl.pxd
-+++ b/src/sage/libs/singular/decl.pxd
-@@ -170,7 +170,7 @@ cdef extern from "singular/Singular/libsingular.h":
-
- int n_NumberOfParameters(const n_Procs_s* r)
-
-- ctypedef struct poly "polyrec":
-+ ctypedef struct poly "spolyrec":
- poly *next
- number *coef
- unsigned long exp[1]
-@@ -630,9 +630,13 @@ cdef extern from "singular/Singular/libsingular.h":
- # return p*q, destroys p and q
- poly *p_Mult_q(poly *p, poly *q, ring *r)
-
-+ # polynomial division, ignoring the rest
-+ # via singclap_pdivide resp. idLift, destroys p,q
-+ poly *p_Divide(poly *p, poly *q, ring *r)
-+
- # divide monomial p by monomial q, p,q const
-
-- poly *pDivide(poly *p,poly *q)
-+ poly *pMDivide(poly *p,poly *q)
-
- # return the i-th power of p; p destroyed, requires global ring
-
-diff --git a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
-index 2a8d9ae021..aeff53af6c 100644
---- a/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
-+++ b/src/sage/rings/polynomial/multi_polynomial_libsingular.pyx
-@@ -190,8 +190,8 @@ from sage.libs.singular.decl cimport (
- n_IsUnit, n_Invers,
- p_ISet, rChangeCurrRing, p_Copy, p_Init, p_SetCoeff, p_Setm, p_SetExp, p_Add_q,
- p_NSet, p_GetCoeff, p_Delete, p_GetExp, pNext, rRingVar, omAlloc0, omStrDup,
-- omFree, pDivide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy,
-- pDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy,
-+ omFree, pMDivide, p_Divide, p_SetCoeff0, n_Init, p_DivisibleBy, pLcm, p_LmDivisibleBy,
-+ pMDivide, p_IsConstant, p_ExpVectorEqual, p_String, p_LmInit, n_Copy,
- p_IsUnit, p_Series, p_Head, idInit, fast_map_common_subexp, id_Delete,
- p_IsHomogeneous, p_Homogen, p_Totaldegree,pLDeg1_Totaldegree, singclap_pdivide, singclap_factorize,
- idLift, IDELEMS, On, Off, SW_USE_CHINREM_GCD, SW_USE_EZGCD,
-@@ -1693,8 +1693,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base):
- if not g._poly:
- raise ZeroDivisionError
-
-- if r!=currRing: rChangeCurrRing(r) # pDivide
-- res = pDivide(f._poly, g._poly)
-+ if r!=currRing: rChangeCurrRing(r) # pMDivide
-+ res = pMDivide(f._poly, g._poly)
- if coeff:
- if r.cf.type == n_unknown or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf):
- n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf)
-@@ -1853,8 +1853,8 @@ cdef class MPolynomialRing_libsingular(MPolynomialRing_base):
- and (g) \
- and g.parent() is self \
- and p_LmDivisibleBy((g)._poly, m, r):
-- if r!=currRing: rChangeCurrRing(r) # pDivide
-- flt = pDivide(f._poly, (g)._poly)
-+ if r!=currRing: rChangeCurrRing(r) # pMDivide
-+ flt = pMDivide(f._poly, (g)._poly)
- #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((g)._poly, r), r), r)
- p_SetCoeff(flt, n_Init(1, r), r)
- return new_MP(self,flt), g
-@@ -4023,16 +4023,6 @@ cdef class MPolynomial_libsingular(MPolynomial):
- Traceback (most recent call last):
- ...
- NotImplementedError: Division of multivariate polynomials over non fields by non-monomials not implemented.
--
-- TESTS::
--
-- sage: P. = ZZ[]
-- sage: p = 3*(-x^8*y^2 - x*y^9 + 6*x^8*y + 17*x^2*y^6 - x^3*y^2)
-- sage: q = 7*(x^2 + x*y + y^2 + 1)
-- sage: p*q//q == p
-- True
-- sage: p*q//p == q
-- True
- """
- cdef MPolynomialRing_libsingular parent = self._parent
- cdef ring *r = self._parent_ring
-@@ -4052,13 +4042,18 @@ cdef class MPolynomial_libsingular(MPolynomial):
- _right = right
-
- if r.cf.type != n_unknown:
-+ if r.cf.type == n_Z:
-+ P = parent.change_ring(RationalField())
-+ f = P(self)//P(right)
-+ CM = list(f)
-+ return parent(sum([c.floor()*m for c,m in CM]))
- if _right.is_monomial():
- p = _self._poly
- quo = p_ISet(0,r)
-- if r != currRing: rChangeCurrRing(r) # pDivide
-+ if r != currRing: rChangeCurrRing(r) # pMDivide
- while p:
- if p_DivisibleBy(_right._poly, p, r):
-- temp = pDivide(p, _right._poly)
-+ temp = pMDivide(p, _right._poly)
- p_SetCoeff0(temp, n_Copy(p_GetCoeff(p, r), r), r)
- quo = p_Add_q(quo, temp, r)
- p = pNext(p)
-@@ -4794,6 +4789,8 @@ cdef class MPolynomial_libsingular(MPolynomial):
- sage: p = -x*y + x*z + 54*x - 2
- sage: (5*p^2).lcm(3*p) == 15*p^2
- True
-+ sage: lcm(2*x,2*x*y)
-+ 2*x*y
- """
- cdef ring *_ring = self._parent_ring
- cdef poly *ret
-@@ -4821,9 +4818,7 @@ cdef class MPolynomial_libsingular(MPolynomial):
- if _ring!=currRing: rChangeCurrRing(_ring) # singclap_gcd
- gcd = singclap_gcd(p_Copy(self._poly, _ring), p_Copy(_g._poly, _ring), _ring )
- prod = pp_Mult_qq(self._poly, _g._poly, _ring)
-- ret = singclap_pdivide(prod , gcd , _ring)
-- p_Delete(&prod, _ring)
-- p_Delete(&gcd, _ring)
-+ ret = p_Divide(prod, gcd, _ring)
- if count >= 20:
- sig_off()
- return new_MP(self._parent, ret)
-@@ -4866,7 +4861,7 @@ cdef class MPolynomial_libsingular(MPolynomial):
- sage: f.quo_rem(y)
- (2*x^2, x + 1)
- sage: f.quo_rem(3*x)
-- (2*x*y + 1, -4*x^2*y - 2*x + 1)
-+ (0, 2*x^2*y + x + 1)
-
- TESTS::
-
-@@ -4888,7 +4883,7 @@ cdef class MPolynomial_libsingular(MPolynomial):
- if right.is_zero():
- raise ZeroDivisionError
-
-- if not self._parent._base.is_field() and not is_IntegerRing(self._parent._base):
-+ if not self._parent._base.is_field():
- py_quo = self//right
- py_rem = self - right*py_quo
- return py_quo, py_rem
-diff --git a/src/sage/rings/polynomial/plural.pyx b/src/sage/rings/polynomial/plural.pyx
-index d5439f7f08..ad20ebcca0 100644
---- a/src/sage/rings/polynomial/plural.pyx
-+++ b/src/sage/rings/polynomial/plural.pyx
-@@ -998,7 +998,7 @@ cdef class NCPolynomialRing_plural(Ring):
- if not g._poly:
- raise ZeroDivisionError
-
-- res = pDivide(f._poly,g._poly)
-+ res = pMDivide(f._poly,g._poly)
- if coeff:
- if (r.cf.type == n_unknown) or r.cf.cfDivBy(p_GetCoeff(f._poly, r), p_GetCoeff(g._poly, r), r.cf):
- n = r.cf.cfDiv( p_GetCoeff(f._poly, r) , p_GetCoeff(g._poly, r), r.cf)
-@@ -1193,7 +1193,7 @@ cdef class NCPolynomialRing_plural(Ring):
- if isinstance(g, NCPolynomial_plural) \
- and (g) \
- and p_LmDivisibleBy((g)._poly, m, r):
-- flt = pDivide(f._poly, (g)._poly)
-+ flt = pMDivide(f._poly, (g)._poly)
- #p_SetCoeff(flt, n_Div( p_GetCoeff(f._poly, r) , p_GetCoeff((g)._poly, r), r), r)
- p_SetCoeff(flt, n_Init(1, r), r)
- return new_NCP(self,flt), g
-diff --git a/src/sage/rings/polynomial/polynomial_singular_interface.py b/src/sage/rings/polynomial/polynomial_singular_interface.py
-index 9331169f8b..f753610fd3 100644
---- a/src/sage/rings/polynomial/polynomial_singular_interface.py
-+++ b/src/sage/rings/polynomial/polynomial_singular_interface.py
-@@ -81,8 +81,8 @@ class PolynomialRing_singular_repr:
- sage: R. = PolynomialRing(CC)
- sage: singular(R)
- polynomial ring, over a field, global ordering
-- // coefficients: float[I](complex:15 digits, additional 0 digits)/(I^2+1)
-- // number of vars : 2
-+ // coefficients: real[I](complex:15 digits, additional 0 digits)/(I^2+1)
-+ // number of vars : 2
- // block 1 : ordering dp
- // : names x y
- // block 2 : ordering C
-@@ -90,8 +90,8 @@ class PolynomialRing_singular_repr:
- sage: R. = PolynomialRing(RealField(100))
- sage: singular(R)
- polynomial ring, over a field, global ordering
-- // coefficients: float
-- // number of vars : 2
-+ // coefficients: Float()
-+ // number of vars : 2
- // block 1 : ordering dp
- // : names x y
- // block 2 : ordering C
diff --git a/pkgs/applications/science/math/sage/patches/spkg-scripts.patch b/pkgs/applications/science/math/sage/patches/spkg-scripts.patch
deleted file mode 100644
index 4d37998b288..00000000000
--- a/pkgs/applications/science/math/sage/patches/spkg-scripts.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-commit f02714d4aea80e17cb8df62bab75d7c1a1b61a8e
-Author: Timo Kaufmann
-Date: Mon Jul 9 18:26:18 2018 +0200
-
- Don't attempt to create dirs when showing pkg info
-
- The script dir cannot be assumed to be writeable after installation.
-
-diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg
-index f3e02aeae5..190d558ad1 100755
---- a/build/bin/sage-spkg
-+++ b/build/bin/sage-spkg
-@@ -167,14 +167,6 @@ if [ -z "$SAGE_BUILD_DIR" ]; then
- export SAGE_BUILD_DIR="$SAGE_LOCAL/var/tmp/sage/build"
- fi
-
--for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS"; do
-- mkdir -p "$dir"
-- if [ $? -ne 0 ]; then
-- error_msg "Error creating directory $dir"
-- exit 1
-- fi
--done
--
-
- # Remove '.' from PYTHONPATH, which may also come from SAGE_PATH, to avoid
- # trouble with setuptools / easy_install (cf. #10192, #10176):
-@@ -563,11 +555,13 @@ fi
- # Setup directories
- ##################################################################
-
--mkdir -p "$SAGE_BUILD_DIR"
--if [ $? -ne 0 ]; then
-- error_msg "Error creating directory $SAGE_BUILD_DIR"
-- exit 1
--fi
-+for dir in "$SAGE_SPKG_INST" "$SAGE_SPKG_SCRIPTS" "$SAGE_BUILD_DIR"; do
-+ mkdir -p "$dir"
-+ if [ $? -ne 0 ]; then
-+ error_msg "Error creating directory $dir"
-+ exit 1
-+ fi
-+done
-
- # Trac #5852: check write permissions
- if [ ! -w "$SAGE_BUILD_DIR" ]; then
diff --git a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch b/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch
deleted file mode 100644
index febab370277..00000000000
--- a/pkgs/applications/science/math/sage/patches/test-in-tmpdir.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-diff --git a/src/sage/repl/ipython_kernel/install.py b/src/sage/repl/ipython_kernel/install.py
-index aa23c8405d..8a87de0591 100644
---- a/src/sage/repl/ipython_kernel/install.py
-+++ b/src/sage/repl/ipython_kernel/install.py
-@@ -112,7 +112,7 @@ class SageKernelSpec(object):
- EXAMPLES::
-
- sage: from sage.repl.ipython_kernel.install import SageKernelSpec
-- sage: spec = SageKernelSpec()
-+ sage: spec = SageKernelSpec(prefix = tmp_dir())
- sage: spec.use_local_mathjax()
- sage: mathjax = os.path.join(spec.nbextensions_dir, 'mathjax')
- sage: os.path.isdir(mathjax)
-@@ -129,7 +129,7 @@ class SageKernelSpec(object):
- EXAMPLES::
-
- sage: from sage.repl.ipython_kernel.install import SageKernelSpec
-- sage: spec = SageKernelSpec()
-+ sage: spec = SageKernelSpec(prefix = tmp_dir())
- sage: spec.use_local_jsmol()
- sage: jsmol = os.path.join(spec.nbextensions_dir, 'jsmol')
- sage: os.path.isdir(jsmol)
-@@ -146,7 +146,7 @@ class SageKernelSpec(object):
- EXAMPLES::
-
- sage: from sage.repl.ipython_kernel.install import SageKernelSpec
-- sage: spec = SageKernelSpec()
-+ sage: spec = SageKernelSpec(prefix = tmp_dir())
- sage: spec.use_local_threejs()
- sage: threejs = os.path.join(spec.nbextensions_dir, 'threejs')
- sage: os.path.isdir(threejs)
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index f74da33f402..f217a7a0cae 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -3,35 +3,17 @@
, fetchpatch
}:
stdenv.mkDerivation rec {
- version = "8.3";
+ version = "8.4";
name = "sage-src-${version}";
src = fetchFromGitHub {
owner = "sagemath";
repo = "sage";
rev = version;
- sha256 = "0mbm99m5xry21xpi4q3q96gx392liwbifywf5awvl0j85a7rkfyx";
+ sha256 = "0gips1hagiz9m7s21bg5as8hrrm2x5k47h1bsq0pc46iplfwmv2d";
};
nixPatches = [
- # https://trac.sagemath.org/ticket/25809
- ./patches/spkg-scripts.patch
-
- # https://trac.sagemath.org/ticket/25309
- (fetchpatch {
- name = "spkg-paths.patch";
- url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69&id=a86151429ccce1ddd085e8090ada8ebdf02f3310";
- sha256 = "1xb9108rzzkdhn71vw44525620d3ww9jv1fph5a77v9y7nf9wgr7";
- })
- (fetchpatch {
- name = "maxima-fas.patch";
- url = "https://git.sagemath.org/sage.git/patch/?h=97f06fddee920399d4fcda65aa9b0925774aec69";
- sha256 = "14s50yg3hpw9cp3v581dx7zfmpm2j972im7x30iwki8k45mjvk3i";
- })
-
- # https://trac.sagemath.org/ticket/25722
- ./patches/test-in-tmpdir.patch
-
# https://trac.sagemath.org/ticket/25358
(fetchpatch {
name = "safe-directory-test-without-patch.patch";
@@ -45,46 +27,9 @@ stdenv.mkDerivation rec {
# https://trac.sagemath.org/ticket/25316
# https://github.com/python/cpython/pull/7476
./patches/python-5755-hotpatch.patch
-
- # https://trac.sagemath.org/ticket/25315
- (fetchpatch {
- name = "find-libraries-in-dyld-library-path.patch";
- url = "https://git.sagemath.org/sage.git/patch/?h=20d4593876ce9c6004eac2ab6fd61786d0d96a06";
- sha256 = "1k3afq3qlzmgqwx6rzs5wv153vv9dsf5rk8pi61g57l3r3npbjmc";
- })
-
- # https://trac.sagemath.org/ticket/25345
- # (upstream patch doesn't apply on 8.2 source)
- ./patches/dochtml-optional.patch
-
- # work with pari with threads enabled at compile time (disable them at runtime)
- # https://trac.sagemath.org/ticket/26002
- ./patches/pari-no-threads.patch
];
packageUpgradePatches = [
- (fetchpatch {
- name = "cypari2-1.2.1.patch";
- url = "https://git.sagemath.org/sage.git/patch/?h=62fe6eb15111327d930336d4252d5b23cbb22ab9";
- sha256 = "1xax7vvs8h4xip16xcsp47xdb6lig6f2r3pl8cksvlz8lhgbyxh2";
- })
-
- # matplotlib 2.2.2 deprecated `normed` (replaced by `density`).
- # This patch only ignores the warning. It would be equally easy to fix it
- # (by replacing all mentions of `normed` by `density`), but its better to
- # stay close to sage upstream. I didn't open an upstream ticket about it
- # because the matplotlib update also requires a new dependency (kiwisolver)
- # and I don't want to invest the time to learn how to add it.
- ./patches/matplotlib-normed-deprecated.patch
-
- # Update to 20171219 broke the doctests because of insignificant precision
- # changes, make the doctests less fragile.
- # I didn't open an upstream ticket because its not entirely clear if
- # 20171219 is really "released" yet. It is listed on the github releases
- # page, but not marked as "latest release" and the homepage still links to
- # the last version.
- ./patches/eclib-regulator-precision.patch
-
# New glpk version has new warnings, filter those out until upstream sage has found a solution
# https://trac.sagemath.org/ticket/24824
./patches/pari-stackwarn.patch # not actually necessary since tha pari upgrade, but necessary for the glpk patch to apply
@@ -94,66 +39,15 @@ stdenv.mkDerivation rec {
stripLen = 1;
})
- (fetchpatch {
- name = "matplotlib-2.2.2";
- url = "https://git.sagemath.org/sage.git/patch?id=0d6244ed53b71aba861ce3d683d33e542c0bf0b0";
- sha256 = "15x4cadxxlsdfh2sblgagqjj6ir13fgdzixxnwnvzln60saahb34";
- })
-
- (fetchpatch {
- name = "scipy-1.1.0";
- url = "https://git.sagemath.org/sage.git/patch?id=e0db968a51678b34ebd8d34906c7042900272378";
- sha256 = "0kq5zxqphhrmavrmg830wdr7hwp1bkzdqlf3jfqfr8r8xq12qwf7";
- })
-
# https://trac.sagemath.org/ticket/25260
./patches/numpy-1.15.1.patch
- # https://trac.sagemath.org/ticket/25862
- ./patches/eclib-20180710.patch
-
- # https://trac.sagemath.org/ticket/24735
- ./patches/singular-4.1.1p2.patch
-
- # https://trac.sagemath.org/ticket/25567 and dependency #25635
- (fetchpatch {
- name = "pari-upgrade-dependency.patch";
- url = "https://git.sagemath.org/sage.git/patch/?id=6995e7cae1b3476ad0145f8dfc897cf91f0c3c4d";
- sha256 = "1dvhabl1c9pwd9xkjvbjjg15mvb14b24p1f3cby1mlqk34d4lrs6";
- })
- (fetchpatch {
- name = "pari-2.11.0.patch";
- url = "https://git.sagemath.org/sage.git/patch/?id=7af4748cab37d651eaa88be501db88f4a5ffc584";
- sha256 = "13f740ly3c19gcmhjngiycvmc3mcfj61y00i6jv0wmfgpm2z3ank";
- })
-
# ntl upgrade
(fetchpatch {
name = "lcalc-c++11.patch";
url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sagemath-lcalc-c++11.patch?h=packages/sagemath&id=0e31ae526ab7c6b5c0bfacb3f8b1c4fd490035aa";
sha256 = "0p5wnvbx65i7cp0bjyaqgp4rly8xgnk12pqwaq3dqby0j2bk6ijb";
})
-
- # cddlib 0.94i -> 0.94j
- (fetchpatch {
- name = "cddlib-0.94j.patch";
- url = "https://git.sagemath.org/sage.git/patch/?id=2ab1546b3e21d1d0ab3b4fcd58576848b3a2d888";
- sha256 = "1c5gnasq7y9xxj762bn79bis0zi8d9bgg7jzlf64ifixsrc5cymb";
- })
-
- # arb 2.13.0 -> 2.14.0
- (fetchpatch {
- name = "arb-2.14.0.patch";
- url = "https://git.sagemath.org/sage.git/patch?id2=8.4.beta0&id=8bef4fd2876a61969b516fe4eb3b8ad7cc076c5e";
- sha256 = "00p3hfsfn3w2vxgd9fjd23mz7xfxjfravf8ysjxkyd657jbkpjmk";
- })
-
- # https://trac.sagemath.org/ticket/26117
- (fetchpatch {
- name = "sympy-1.2.patch";
- url = "https://git.sagemath.org/sage.git/patch?id2=8.4.beta2&id=d94a0a3a3fb4aec05a6f4d95166d90c284f05c36";
- sha256 = "0an2xl1pp3jg36kgg2m1vb7sns7rprk1h3d0qy1gxwdab6i7qnvi";
- })
];
patches = nixPatches ++ packageUpgradePatches ++ [
diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix
index abcefba5e26..d26f5dad724 100644
--- a/pkgs/applications/science/math/sage/sagelib.nix
+++ b/pkgs/applications/science/math/sage/sagelib.nix
@@ -47,6 +47,8 @@
, singular
, pip
, jupyter_core
+, libhomfly
+, libbraiding
}:
buildPythonPackage rec {
@@ -109,6 +111,8 @@ buildPythonPackage rec {
pip
cython
cysignals
+ libhomfly
+ libbraiding
];
buildPhase = ''